In sql compare you can uncheck the option and it will detect synonyms that differ only by the server or database. I don't see any way to disable that option in sql source control so when i change my synonym it isn't picking it up as a change so I can't check it in.

In the latest version of SQL Source Control there is no option to configure the comparisons performed by the product (unlike SQL Compare - as you mentioned).

However, we are currently working on adding a comparison options configuration file to SQL Source Control that will allow you to detect synonym changes (and change many of the other options available in SQL Compare).

We are hoping to release this in the next few weeks via our 'Check For Updates' mechanism. I will add a post to this thread when that build is available.

Our plan in the future is to provide an options dialog to allow users to configure the comparison options that are changed most often, but we believe this configuration file procedure should help users in the interim.

If you'd like to see an options dialog exposing these settings in SQL Source Control, please vote on the associated Idea on our UserVoice site. It'd be great if you could also leave a comment indicating which specific options you'd like to see in the dialog.